Galapagos Cruise or Island Hopping – What’s Best?

One of the first questions we get from clients planning their Galapagos trip is: “Should I do a cruise, or go island hopping?”

And honestly, it’s a great question — both offer completely different ways to explore this incredible place.

We can honestly tell you there’s no universal ‘best’ option. But there is a best choice for you — and we are here to help you figure out what that is.

What’s the Difference?

In a nutshell:

Galapagos cruises are small-ship (most of the time, there are some bigger ones too!) expeditions that sail between the islands, usually over 4 to 8 days. You sleep onboard and visit new sites each day — many of which are only accessible by boat.
Island hopping is land-based. You stay in hotels on a few of the main inhabited islands — usually Santa Cruz, San Cristóbal, and sometimes Isabela — and take day trips to nearby visitor sites.

Each has its advantages. It all depends on your travel style, budget, and how you want to experience the islands.

Why Choose a Galapagos Cruise?

If you want to experience the Galapagos as fully as possible, a cruise is the way to go. You’ll travel overnight between islands, visit remote sites that day-trippers simply can’t reach, and enjoy early morning landings with hardly another soul in sight.

I still remember one morning, just after sunrise, stepping ashore on Española Island. No other boats in sight. Dozens of marine iguanas warming themselves on black lava, and a waved albatross just a few feet away. That’s the kind of magic cruises unlock.

Pros:

Access to remote islands like Genovesa, Fernandina and Española — home to species you won’t see on day trips.
More time exploring: You’re often the first to land in the morning and the last to leave in the evening.
All-inclusive simplicity: Itinerary, meals, excursions — everything is taken care of.
Immersive experience: You’re completely in the moment, surrounded by nature 24/7.

Cons:

Usually higher cost: Cruises tend to be more expensive than land-based trips (though they include far more like all you meals and excursions led by the same naturalist guide).
Less freedom: Itineraries are fixed, and there’s no popping into town or choosing your own restaurant.
Motion at sea: Even though most crossings happen at night, you do feel the movement — something to keep in mind if you’re sensitive to it.

Why Choose Island Hopping?

Island hopping works well if you prefer a bit more independence and want to mix wildlife with a more relaxed, cultural vibe. You’ll base yourself in small towns like Puerto Ayora or Puerto Villamil, stay in local hotels, and head out each day on guided excursions.

It’s also a great choice for families or anyone who prefers being on land at night.

Pros:

More flexibility: Choose where to eat, what to do in the evenings, and how much downtime you want.
Better for certain budgets: Accommodation and meals can be tailored to fit your spend, and you can travel for fewer days if needed.
Cultural connection: You’ll meet local people, shop in small markets, and get a feel for life on the islands.

Cons:

Limited range: You’ll only be able to visit sites close to the main islands — some of the more iconic wildlife spots are out of reach.
More time in transit: Day boats involve longer travel times and early starts, and you’ll return to the same hotel each night.
Less immersion: You’re not out on the water overnight or waking up to wild, remote landscapes.

So, which one is best?

If your priority is seeing as much wildlife as possible, including rare species and remote islands, choose a cruise. The experience is seamless, immersive, and maximised for time in nature. For many of my clients, this is the trip of a lifetime — and a cruise gives them the most memorable version of it.

If you prefer flexibility, a slightly lower budget, and being based on land so you can enjoy the cultural side of the Galapagos, island hopping could suit you better. You’ll still see amazing wildlife — sea lions, marine iguanas, giant tortoises — just in fewer places.

What is Fleewinter’s recommendation and how did we experience the Galapagos?

Do a bit of both! If you are not short on time, mix a cruise with a few days on land. You will enjoy the best of both worlds!

That’s how we lived our Galapagos experience and we cannot recommend it enough. We didn’t miss out on either the wildlife and the cultural side of these islands. People live here, and they go about their daily business and it is fascinating to watch. If you only do a cruise you will miss out on this very enriching experience. Also, some inland excursions (for example, the Sierra Negra Volcano hike on Isabela) are not included in cruise itineraries.

On our trip, after the cruise all other passengers were waving goodbye at the airport, whilst we went back to Puerto Ayora for a few nights extension to do some diving and immerse ourselves in the culture of the island. These few days are one of our best memories of our Galapagos adventure!

Get in touch to get the best recommendations and book and unforgettable holiday!

Don’t miss the buzz of Puerto Ayora’s fish market!

This guide was created by Val, specialist in tailor-made Ecuador and Galapagos adventures.

Quito

Capital of the country and one of the continent's most beautifully preserved colonial cities.

Cotopaxi volcano

One of the world's most photogenic volcanoes! Visit the beautiful and eponymous park.

Otavalo

Charming town, full of indigenous culture and a famous market.

Mindo cloud forest

A birdwatcher paradise!

Coca

The gateway to the an immersive experience into Ecuador's pristine Amazon rainforest.

Banos

Charming town with a lovely square, wonderful nature around and capital of adrenaline sports (if you are so inclined).

Riobamba

A lovely town on the Avenue of volcanoes. Enjoy a 'hornado' (pig roast) al mercado La Merced.
The town is also the getaway for tours to Chimborazo volcano.

Cuenca

Beautiful Cuenca deserves a special mentions as it is one of the most beautiful colonial cities in the continent. The lovely square is gorgeous and the whole city is welcoming and friendly. Go and visit the outdoor flower market for an injection of colour!

Guayaquil

Often overlooked, Guayaquil is mainly an arrival or departure point. However, the malecon is worth having a walk on, and La Penas is the oldest and most pleasant part of the city.

The Galapagos Islands

The Galápagos Islands are famed for their unique wildlife and role in Charles Darwin’s theory of evolution. They are located about 1,000 km (620 miles) off Ecuador’s coast, they feature volcanic landscapes, pristine beaches, and diverse ecosystems. Iconic species include giant tortoises, marine iguanas, blue-footed boobies, and Galápagos penguins. The islands offer a rare glimpse of nature’s adaptability in an isolated paradise and should be on everyone's bucket list.